Description Usage Arguments Value Author(s) See Also Examples
Segments normalized copy number data.
1 2 
object 
An object of class QDNAseqCopyNumbers. 
smoothBy 
An optional integer value to perform smoothing before
segmentation by taking the mean of every smoothBy bins, and then
segment those means. Default ( 
alpha 
Significance levels for the test to accept changepoints. Default is 1e10. 
undo.splits 
A character string specifying how changepoints are to be undone, if at all. Default is "sdundo", which undoes splits that are not at least this many SDs apart. Other choices are "prune", which uses a sum of squares criterion, and "none". 
undo.SD 
The number of SDs between means to keep a split if undo.splits="sdundo". Default is 1.0. 
force 
Whether to force execution when it causes removal of downstream calling results. 
transformFun 
A function to transform the data with. This can be
the default "log2" for log2(x + .Machine$double.xmin),
"sqrt" for the Anscombe transform of sqrt(x * 3/8) which
stabilizes the variance, "none" for no transformation, or any
R function that performs the desired transformation and also its
inverse when called with parameter 
seeds 
An optional integer vector of seeds for random number
generation, recycled as needed. Normally, the segmentation process is
split by sample, and provided seeds also used per sample. But when
smoothing is performed (or in the the special case of

... 
Additional arguments passed to 
Returns an object of class QDNAseqCopyNumbers with segmentation results added.
Ilari Scheinin
Internally, segment
of the DNAcopy package,
which implements the CBS method, is used to segment the data.
1 2 3 4 5 6 7 8  data(LGG150)
readCounts < LGG150
readCountsFiltered < applyFilters(readCounts)
readCountsFiltered < estimateCorrection(readCountsFiltered)
copyNumbers < correctBins(readCountsFiltered)
copyNumbersNormalized < normalizeBins(copyNumbers)
copyNumbersSmooth < smoothOutlierBins(copyNumbersNormalized)
copyNumbersSegmented < segmentBins(copyNumbersSmooth)

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